Started on 2024-12-15 20:24:11

Reference genome

Coverage statistics

Mean coverage per contig

Cov dist per base

Analysis of the global distribution and motif of DNA modification data

Ratio Modified bases / Sequenced bases

Modification sequence logo with enrichment score

## [1] "6850_SN_A1"

## [1] "SB0804_TSB_F1"

## [1] "SB0804_TSB_F2"

## [1] "SB0804_TSB_F3"

## [1] "SB1002_SN_G1"

## [1] "SB1002_SN_G2"

## [1] "SB1002_SN_G3"

## [1] "SB1002_TSB_H1"

## [1] "SB1002_TSB_H2"

## [1] "SB1002_TSB_H3"

## [1] "6850_SN_A2"

## [1] "6850_SN_A3"

## [1] "6850_TSB_B1"

## [1] "6850_TSB_B2"

## [1] "6850_TSB_B3"

## [1] "SB0804_SN_E1"

## [1] "SB0804_SN_E2"

## [1] "SB0804_SN_E3"

Filtering the DNA modification data using False Discovery Rate estimations

## [1] "6850_SN_A1"

## [1] "SB0804_TSB_F1"

## [1] "SB0804_TSB_F2"

## [1] "SB0804_TSB_F3"

## [1] "SB1002_SN_G1"

## [1] "SB1002_SN_G2"

## [1] "SB1002_SN_G3"

## [1] "SB1002_TSB_H1"

## [1] "SB1002_TSB_H2"

## [1] "SB1002_TSB_H3"

## [1] "6850_SN_A2"

## [1] "6850_SN_A3"

## [1] "6850_TSB_B1"

## [1] "6850_TSB_B2"

## [1] "6850_TSB_B3"

## [1] "SB0804_SN_E1"

## [1] "SB0804_SN_E2"

## [1] "SB0804_SN_E3"

Only AG motifs reach a FDR estimation below 5% (using a score threshold of somewhere above a 1300)

Analysis of the DNA modification patterns within genomic annotations

Counts by feature

## [1] "6850_SN_A1"

## [1] "SB0804_TSB_F1"

## [1] "SB0804_TSB_F2"

## [1] "SB0804_TSB_F3"

## [1] "SB1002_SN_G1"

## [1] "SB1002_SN_G2"

## [1] "SB1002_SN_G3"

## [1] "SB1002_TSB_H1"

## [1] "SB1002_TSB_H2"

## [1] "SB1002_TSB_H3"

## [1] "6850_SN_A2"

## [1] "6850_SN_A3"

## [1] "6850_TSB_B1"

## [1] "6850_TSB_B2"

## [1] "6850_TSB_B3"

## [1] "SB0804_SN_E1"

## [1] "SB0804_SN_E2"

## [1] "SB0804_SN_E3"

Counts within feature

## [1] "6850_SN_A1"

## [1] "SB1002_SN_G1"

## [1] "SB1002_SN_G2"

## [1] "SB1002_SN_G3"

## [1] "6850_SN_A2"

## [1] "6850_SN_A3"